Make templates consistent with how links are checked- v2

This is a replacement for #65 - it splits the commit to only include changes to .md and .html files.

The old branch is preserved for posterity- we will be discarding the affected functions in tools/check anyway, so there is no need to merge that file to the main repo. If you'd like to try that modified version of the validator, it will remain on the old branch until this pull request is closed.
I admit to being puzzled by this.  Can you try the build with this branch (and gh-pages) to see if you get the same result?

This branch should be fully synced with swcarpentry/gh-pages ... but when I run `make very-clean; make clean; make preview` on gh-pages, the span classes are inserted correctly. 

Even though this branch is based off of the most recent gh-pages, running the same build sequence on this branch omits the span tags. (as shown here) What is different?